New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
22 months
265
12
88235
7199
60
63
Parser of scientific names (...) !
Dmitry Mozzherin
2 weeks
18
5
47146
5182
0
8
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
2 weeks
5
1
40727
3395
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
10 months
14
11
37266
3467
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
4 weeks
17
6
35815
6206
0
12
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
4 weeks
2
...
28860
2271
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
12 months
13
1
24304
2592
Gadgets for bioinformatics (...)
Shintaro Katayama
21 months
...
23614
3359
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
23340
2239
0
0
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
4
22618
1533
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
12 months
22049
1548
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
5 days
67
41
20717
2720
3
203
Create pretty svg-format images of features, gene models (...)
Dan MacLean
14 months
9
5
19016
4363
0
0
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
18302
1500
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
17478
2068
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
15583
1241
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
15162
1819
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
14514
1216
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
4 months
12
...
14176
2114
0
2
A simple obo file handler (...) !
mjy
3 years
4
...
13648
1047
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
10903
1077
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
10 months
7
5
10723
1170
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
10 months
8
20
10602
1378
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
11 weeks
12
2
10283
2386
Data mining algorithms for jRuby (...)
arrigonialberto86
18 months
14
3
9250
1678
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
1
...
9207
918
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9133
749
0
0
Low memory sequence emitters (...)
Pjotr Prins
10 months
8
1
8783
916
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
8706
560
0
0
Build genome output files (...)
Michael Barton
19 months
5
...
8247
559
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
7 months
2
...
8242
954
Ruby support for the baclava file format (...) !
Robert Haines
12 months
1
...
8165
530
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
7978
595
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7836
521
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7710
763
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
21 months
8
...
7532
726
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
7487
629
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
22 months
5
...
7439
896
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7363
755
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7321
702
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7297
624
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
12 months
...
7292
589
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6800
476
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
3 weeks
2
1
6713
2769
0
18
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6683
546
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
30
14
6420
520
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
6090
462
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5747
723
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
5398
460
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
19 months
11
2
5345
1059
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5322
433
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
5192
471
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4997
477
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
23 months
2
1
4961
612
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
38
5
4841
255
0
0
Ruby binding for samtools tabix (...)
throwern
18 months
3
...
4690
601
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
4 weeks
4
3
4674
1071
0
9
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4175
462
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4115
467
0
0
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4094
465
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4085
448
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4073
309
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4040
312
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
11 weeks
...
3976
1476
0
6
Fast multi-threaded vcf parser (...)
Pjotr Prins
3 months
16
7
3877
1405
0
47
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3812
336
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3779
343
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3517
303
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
18 months
3464
607
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3347
315
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3310
455
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3296
311
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
22 months
...
3197
469
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
19 months
1
...
3188
462
0
0
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
3 weeks
...
3141
1445
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2960
310
A protparam compatible utility for BioRuby (...)
hryk
2 years
1
...
2897
301
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2801
305
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
9 months
3
16
2583
411
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
12 months
1
...
2317
609
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2105
138
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2102
163
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2098
160
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2021
159
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
11 weeks
1
1986
1134
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
13 months
6
...
1968
185
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1840
153
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1824
147
Gggenome Ruby client (...)
Mitsuteru Nakao
19 months
1
...
1819
305
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1808
157
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1803
159
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1780
155
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1769
156
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1754
154
Ruby ensembl rest api (...)
Alberto Donizetti
18 months
3
1
1737
306
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1729
153
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1722
166
Biostars data-mining and statistical analysis (...)
Joachim Baran
11 months
1701
476
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1693
148
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1684
157
Generalized linear models for statsample (...)
Ankur Goel
18 months
1683
308
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
...
1675
171
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
4 months
1
1636
809
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1600
168
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
1494
156
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1484
152
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1461
106
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
14 months
...
1428
309
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
14 months
...
1421
322
Bio-repeatmasker (...)
Andrei Rozanski
14 months
1390
304
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
5
...
1315
411
A parser for cigar format alignments (...)
Ben J Woodcroft
13 months
4
...
1254
314
0
0
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1244
164
Web server for bio-samtools (...)
homonecloco
10 months
...
1117
322
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
21 months
2
...
1030
163
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
20 months
...
965
159
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
5 months
914
333
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
9 weeks
813
813
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
90
1
671
219
Mine publications for gene names (...)
Pjotr Prins
13 months
...
637
160
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
3 months
1
...
597
390
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
12 months
570
193
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
8 months
1
...
485
170
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
6 months
...
444
200
0
0
(...) pre
pre
405
29
Tools to work with fasta files, indexed with (...)
homonecloco
5 months
...
404
175
Tools to manipulate blat files from the command (...)
homonecloco
5 months
...
397
171
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
4 months
...
346
182
0
0
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
4 months
...
344
177
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
341
107
Helper methods for reading .delta files (...)
robsyme
5 days
...
306
306
(...) pre
pre
151
36
!
Bioinformatics. aggregate fastqc (quality control for next generation (...) new
Raoul Jean Pierre Bonnal
6 days
...
122
122
!
A pipeline manager (...) new
Francesco Strozzi
2 days
8
10
100
100
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-03-28
**) number of commits on GitHub (last 7 days & last 90 days)